Features:

Multi GPU support:

Yes

BarraCUDA

Description:

Sequence mapping software

Features:

Alignment of short sequencing reads, alignment of indels with gap openings and extensions.

Multi GPU support:

Yes

BEAGLE-lib

Description:

BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.

Multi GPU support:

Yes

Campaign

Description:

An open-source library of GPU-accelerated data clustering algorithms and tools.

Features:

K-means (and Kps-means, a K-means variant for GPUs with parallel sorting for improved performance), K-medoids, K-centers (a K-medoids variant in which medoids are placed only once according to a heuristic), Hierarchical clustering and Self-organizing map.

Multi GPU support:

Single only

CUDASW++

Description:

Open source software for Smith-Waterman protein database searches on GPUs.

Features:

Parallel search of Smith-Waterman database.

Multi GPU support:

Yes

CUSHAW

Description:

Parallelized short read aligner

Features:

Parallel, accurate long read aligner for large genomes

Multi GPU support:

Yes

G-BLASTN

Description:

GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

Features:

Multi GPU support:

NVBowtie

Description:

A largely complete implementation of the Bowtie2 aligner on top of NVBIO.

Features:

Good coverage of Bowtie2 features and comparable quality results.

Multi GPU support:

Yes

PEANUT

Description:

Read mapper for DNA or RNA sequence reads to a known reference genome.

Features:

Achieves supreme sensitivity and speed compared to current state of the art read mappers like BWA MEM, Bowtie2 and RazerS3. PEANUT reports both only the best hits or all hits.

Multi GPU support:

Single only

REACTA

Description:

A modified version of GCTA with improved computational performance, support for Graphics Processing Units (GPUs), and additional features. The purpose of REACTA is to quantify the contribution of genetic variation to phenotypic variation for complex traits.

Features:

Multi GPU support:

Yes

SeqNFind

Description:

SeqNFind® is a powerful tool suite that addresses the need for complete and accurate alignments of many small sequences against entire genomes utilizing a unique hardware/software cluster system for facilitating bioinformatics research in Next Generation sequencing and genomic comparisons.

Features:

Multi GPU support:

DESMOND

Description:

Features:

The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy.

Multi GPU support:

Yes

ESPResSo

Description:

Highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.

Multi GPU support:

Single only

SOP-GPU

Description:

SOP-GPU package, where SOP stands for the Self Organized Polymer Model fully implemented on a GPU, is a scientific software package designed to perform Langevin Dynamics Simulations of the mechanical or thermal unfolding, and mechanical indentation of large biomolecular systems in the experimental subsecond (millisecond-to-second) timescale.

Features:

Langevin dynamics simulations using the coarse-grained Self Organized Polymer (SOP) model, Multiple simulation trajectories can be performed simultaneously on a single GPU, Calpha and Calpha-Cbeta models are supported, Simulations of protein forced unfolding, Novel simulations of nanoindentation in silico, Support for hydrodynamic interactions, Up to ~100 ms of simulation time per day, Systems of up to 1,000,000 amino-acids (on GPUs with 6GB or great memory).

Multi GPU support:

Single only

Quantum Chemistry >

Abinit

Description:

Allows to find total energy, charge density and electronic structure of systems made of electrons and nuclei within DFT.

Features:

Multi GPU support:

BigDFT

Description:

Implements density functional theory by solving the Kohn-Sham equations describing the electrons in a material.

Features:

DFT; Daubechies wavelets, part of Abinit

Multi GPU support:

Yes

CASTEP [In development]

Description:

CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materials proprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc.

Features:

TBD

Multi GPU support:

Yes

CP2K

Description:

Program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems.

Features:

DBCSR (space matrix multiply library)

Multi GPU support:

Yes

GAMESS-UK

Description:

The general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations.

Multi GPU support:

PWMat

Description:

Features:

It can perform extremely fast plane wave DFT calculations based on GPU machines and single precision and double precision mixed algorithm. It deploys the state-of- the-art electronic structure calculation methods with many new features and algorithm innovations. It performs ab initio material science simulations, designed for both theoretical and experimental groups.

Multi GPU support:

Mathworks - MATLAB

Description:

Features:

Support for 200+ of most used MATLAB functions (incl. Signal Processing, Image Processing, Communications Systems, etc).

Multi GPU support:

Yes

NMath Premium

Description:

GPU-accelerated math and statistics for .NET, automatically detects the presence of a CUDA-enabled GPU at runtime and seamlessly redirects appropriate computations to it.

Features:

Automatically offloads computations to the GPU.

Multi GPU support:

Single only

PHYSICS

AWP

Description:

The Anelastic Wave Propagation, AWP- ODC, independently simulates the dynamic rupture and wave propagation that occurs during an earthquake. Dynamic rupture produces friction, traction, slip, and slip rate information on the fault. The moment function is constructed from this fault data and used to initialize wave propagation.

GTC

Description:

Features:

Multi GPU support:

GTC-P

Description:

A development code for optimization of plasma physics. Full science and data sets are included, but in a simplified form to allow performance testing and tuning.

Features:

Optimized with CUDA. OpenACC development underway

Multi GPU support:

Yes

GTS

Description:

Simulates microturbulence and the motion of charged particles and interactions in fusion plasma.

Features:

Push and shift for both electron and ion dynamics

Multi GPU support:

Yes

HACC

Description:

Simulates N-Body Astrophysics

Features:

This code has been optimized with CUDA runs in full production mode.

Multi GPU support:

Yes

* MAESTRO

Description:

A low Mach number stellar hydrodynamics code that can be used to simulate long- time, low-speed flows that would be prohibitively expensive to model using traditional compressible code.

Features:

Gravitational Field Solver

Multi GPU support:

Yes

MILC

Description:

Lattice Quantum Chromodynamics (LQCD) codes simulate how elemental particles are formed and bound by the “strong force” to create larger particles like protons and neutrons.

Features:

Staggered fermions, Krylov solvers, Gauge- link fattening.

Multi GPU support:

Yes

OSIRIS

Description:

Simulates Plasma Physics including Laser interaction

Features:

2 dimensions of the particle push have been optimized with CUDA. Additional optimization is being planned with OpenACC.

Multi GPU support:

Yes

PIConGPU

Description:

A relativistic Particle-in-Cell code that describes the dynamics of a plasma by computing the motion of electrons and ions subject to the Maxwell-Vlasov equation.

Features:

Simulation of laser-wakefield acceleration of electrons.

Multi GPU support:

Yes

PPM

Description:

Piecewise parabolic method, a higher- order extension of Godunov’s method which uses spatial interpolation and allows for a steeper representation of discontinuities, particularly contact discontinuities.

Features:

Turbulent, compressible mixing of gases in the context of stars near the ends of their lives and also in inertial confinement fusion.